Contacts of the strand formed by residues 138 - 145 (chain B) in PDB entry 1QXP
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ILE 138 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B TYR* 3.8 19.4 + - + -
35B LEU* 4.0 17.5 - - + -
36B ARG* 3.8 34.9 - - + +
39B CYS* 5.4 0.2 - - - -
46B PHE* 3.3 42.2 - - + -
135B TYR 4.7 3.7 - - - +
136B ALA* 4.2 9.4 - - + +
137B GLY* 1.3 75.3 - - - +
139B PHE* 1.2 81.9 + - - +
153B VAL* 4.2 11.7 - - + -
154B VAL 3.2 14.1 - - - +
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Residues in contact with PHE 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B TYR* 4.0 3.8 - - - -
87B PHE* 3.4 42.4 - + + -
129B GLN* 3.2 24.7 - - + +
130B SER 4.0 19.3 - - - -
131B PHE* 3.3 28.5 - + - -
135B TYR* 3.7 13.5 - + - -
138B ILE* 1.2 95.2 - - - +
140B HIS* 1.4 62.9 + - - +
141B PHE* 4.6 4.7 - - + -
153B VAL* 3.4 1.9 - - - +
154B VAL* 2.9 34.1 + - + +
156B ASP* 3.8 27.1 - - + -
180B LEU* 3.9 13.2 - - + -
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Residues in contact with HIS 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B TYR* 3.3 50.2 - + + +
126B PRO* 3.4 37.2 - - + +
127B TYR 5.5 1.1 - - - -
129B GLN* 2.9 27.6 + - + -
139B PHE* 1.4 75.7 - - - +
141B PHE* 1.4 68.2 + - - +
142B GLN* 5.5 0.6 + - - -
151B ASP* 2.7 38.6 - - - +
152B VAL 3.0 15.3 - - - +
153B VAL* 3.9 4.0 - - + -
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Residues in contact with PHE 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B PHE* 3.3 30.7 - + - -
124B VAL 3.4 7.9 - - - +
125B VAL* 3.7 25.6 - - + -
126B PRO* 4.2 0.2 - - - -
139B PHE* 4.6 4.0 - - + -
140B HIS* 1.4 86.6 - - - +
142B GLN* 1.3 69.1 + - - +
143B LEU* 3.3 6.4 + - + +
150B VAL 3.4 0.2 - - - +
151B ASP* 4.3 0.4 - - - -
152B VAL* 2.8 37.7 + - - +
154B VAL* 4.9 5.2 - - + -
177B TRP 4.0 2.5 - - - -
180B LEU* 3.6 21.5 - - + -
181B LEU* 3.4 52.3 - - + -
184B ALA* 4.0 24.5 - - + -
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Residues in contact with GLN 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B HIS* 2.9 46.3 + - - +
24B ALA* 4.7 10.8 - - - +
123B ARG 3.9 9.6 - - - +
124B VAL* 3.0 34.5 + - - +
126B PRO* 4.6 14.3 - - + +
140B HIS* 5.5 0.7 + - - -
141B PHE* 1.3 72.3 - - - +
143B LEU* 1.3 63.7 + - - +
149B TRP* 3.9 16.8 - - + -
150B VAL 3.2 7.4 - - - +
151B ASP* 3.1 31.5 - - - +
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Residues in contact with LEU 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B VAL* 3.7 19.7 - - + -
141B PHE* 3.3 8.0 + - + +
142B GLN* 1.3 76.5 - - - +
144B TRP* 1.3 62.3 + - - +
145B GLN* 3.2 16.0 + - + +
149B TRP* 3.9 4.6 - - - -
150B VAL* 2.9 34.2 + - + +
152B VAL* 5.1 3.4 - - + -
181B LEU* 4.3 7.4 - - + +
184B ALA* 4.4 10.8 - - + +
185B TYR* 4.0 41.1 - - + +
188B VAL* 4.5 11.9 - - + -
206B ASP* 3.9 6.3 - - + +
207B PHE* 3.6 36.1 - - + -
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Residues in contact with TRP 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B LEU* 1.3 69.6 - - - +
145B GLN* 1.3 62.0 + - - +
146B PHE 3.8 2.7 - - - -
147B GLY* 3.0 40.8 + - - -
148B GLU 3.3 9.2 - - - -
149B TRP* 3.6 40.0 - + + +
205B GLU* 3.5 32.8 - - + +
206B ASP* 3.1 45.5 + - - +
209B GLY* 3.6 16.4 + - - -
343B LEU* 5.1 4.2 - - - +
414B MET* 3.5 33.9 - - + -
499B LEU* 4.0 7.6 - - + -
501B ARG* 3.1 37.7 - - - -
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Residues in contact with GLN 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B TYR* 5.8 3.3 - - + -
143B LEU* 3.2 12.5 + - + +
144B TRP* 1.3 74.4 + - - +
146B PHE* 1.3 98.0 + - + +
147B GLY 2.8 4.7 + - - -
148B GLU* 2.8 28.5 + - + +
150B VAL* 4.4 21.8 - - + -
185B TYR* 4.6 4.4 - - - -
188B VAL* 3.0 37.9 - - + +
189B ASN* 5.3 3.3 + - - +
206B ASP* 3.0 28.9 + - - +
416B LYS* 5.5 0.3 + - - -
470B ARG* 4.9 0.4 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il